Carole Goble

Sean R. Wilkinson, Johan Gustafsson, Finn Bacall et al.

Computational workflows represent major investments of effort and expertise. As first-class, publishable research objects of their own, they are key to sharing methodological know-how for reuse, reproducibility, and transparency. Thus, the application of the FAIR Principles to workflows is inevitable to enable them to be Findable, Accessible, Interoperable, and Reusable. Making workflows FAIR reduces duplication of effort, assists in the reuse of best practice approaches and community-supported standards, and ensures that workflows as digital objects can support reproducible, robust science. FAIR workflows draw from both FAIR data and software principles, and they help ensure and support data FAIRification. The FAIR Principles emphasize the association of persistent identifiers and machine-actionable metadata with workflows. Implementing the Principles requires a framework with appropriate programmatic protocols and an accompanying ecosystem of services, tools, policies, and best practices, as well the buy-in of existing workflow systems. The European EOSC-Life Workflow Collaboratory is an example of such a digital infrastructure for the Biosciences. It includes a metadata standards framework for describing workflows that is managed and used by dedicated new FAIR workflow services and programmatic APIs for interoperability and metadata access. It includes the WorkflowHub registry and LifeMonitor workflow testing service, and it incorporates existing workflow systems and packaging solutions. Here, we introduce the FAIR Principles for workflows and connect FAIR workflows with the FAIR ecosystems they inhabit with the EOSC-Life Collaboratory as a concrete example. We also introduce other community efforts that are easing the ways that workflows are shared and reused by others, and we discuss how the variations in different workflow settings impact their FAIR perspectives.

Gavin Farrell, Eleni Adamidi, Rafael Andrade Buono et al.

Artificial intelligence (AI) has recently seen transformative breakthroughs in the life sciences, expanding possibilities for researchers to interpret biological information at an unprecedented capacity, with novel applications and advances being made almost daily. In order to maximise return on the growing investments in AI-based life science research and accelerate this progress, it has become urgent to address the exacerbation of long-standing research challenges arising from the rapid adoption of AI methods. We review the increased erosion of trust in AI research outputs, driven by the issues of poor reusability and reproducibility, and highlight their consequent impact on environmental sustainability. Furthermore, we discuss the fragmented components of the AI ecosystem and lack of guiding pathways to best support Open and Sustainable AI (OSAI) model development. In response, this perspective introduces a practical set of OSAI recommendations directly mapped to over 300 components of the AI ecosystem. Our work connects researchers with relevant AI resources, facilitating the implementation of sustainable, reusable and transparent AI. Built upon life science community consensus and aligned to existing efforts, the outputs of this perspective are designed to aid the future development of policy and structured pathways for guiding AI implementation.

Pinar Alper, Khalid Belhajjame, Carole A. Goble

In recent years the need to simplify or to hide sensitive information in provenance has given way to research on provenance abstraction. In the context of scientific workflows, existing research provides techniques to semi automatically create abstractions of a given workflow description, which is in turn used as filters over the workflow's provenance traces. An alternative approach that is commonly adopted by scientists is to build workflows with abstractions embedded into the workflow's design, such as using sub-workflows. This paper reports on the comparison of manual versus semi-automated approaches in a context where result abstractions are used to filter report-worthy results of computational scientific analyses. Specifically; we take a real-world workflow containing user-created design abstractions and compare these with abstractions created by ZOOM UserViews and Workflow Summaries systems. Our comparison shows that semi-automatic and manual approaches largely overlap from a process perspective, meanwhile, there is a dramatic mismatch in terms of data artefacts retained in an abstracted account of derivation. We discuss reasons and suggest future research directions.